Help with a reading count command using HTSeq
I am working on bacterial RNAseq data analysis, here is what I have down:
Bowtie:
bowtie -S reference ~/RNAseq/QC/decompressed_mybacteria.fastq > mybacteria.sam
Htseq:
htseq-count -m intersection-nonempty --stranded=no mybacteria.sam template.gtf > count.sam
My original seq was created by using Hiseq Illumina, paired end.
I know it could be htseq variable I used here is not good.
Anyone can help with this command line? Thank you
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Ram
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flavobacteria •
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flavobacteria •
1 answer
Firstly, I am not sure that this is right command for paired end fastq files , they should be "prefix_1.fastq" and "prefix_2.fastq"
next, I would use featureCount instead of htseq-count, but if you want to use htseq-count, then this is right command.
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Manvendra Singh
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